This report follows the broad definition of a biomarker as a characteristic that can be objectively measured and evaluated as an indicator of normal biological or pathogenic processes as well as pharmacological responses to a therapeutic intervention. Tests based on biomarkers have been around for more than half a century, but interest in their application for diagnostics and drug discovery as well as development has increased remarkably since the beginning of the 21st century. This report describes different types of biomarkers and their discovery using various "-omics" technologies such as proteomics and metabolomics. Molecular diagnostics technologies are used for the discovery of biomarkers and new tests are also based on biomarker.

Currently the most important applications of biomarkers are in drug discovery and development. The role of biomarkers in various therapeutic areas particularly cancer, cardiovascular diseases and disorders of the central nervous system, is described. Biomarkers are useful not only for diagnosis of some of these diseases but also for understanding the pathomechanism as well as a basis for development of therapeutics.

Biomarkers will facilitate the combination of therapeutics with diagnostics and will thus play an important role in the development of personalized medicine. Biomarkers play a role in use of pharmacogenetics, pharmacogenomics and pharmacoproteomics for development of personalized medicine.

Many of the regulatory issues concerning biomarkers are related to genomics, proteomics, molecular diagnostics and pharmacogenomics/pharmacogenetics. Validation of biomarkers and their role in clinical trials is discussed.

Biomarker markets are estimated from 2009 to 2019 according to share of markets for various technologies and applications: proteomics, metabolomics, molecular diagnostics, drug discovery, clinical trials, and bioinformatics. Market values are further split according to therapeutic applications and major geographical areas. Unfulfilled needs in biomarkers are identified as well as the drivers for biomarker markets. Challenges facing the biomarker industry and strategies for developing biomarker markets are discussed.

A large number of companies with varying technical backgrounds are involved in biomarkers and 265 of these are profiled in part 2 of the report with classification into various categories.These also include major pharmaceutical companies. There is tabulation of 479 collaborations between companies and additional academic collaborations are mentioned in the individual profiles of companies. The report is supplemented by 800 references, 62 tables and 12 figures

TABLE OF CONTENTS

0. Executive Summary 19

1. Introduction 21

Definitions 21

Historical aspects of biomarkers 21

Classification of biomarkers 22

Biological marker as response to therapeutic intervention 23

Pharmacokinetic/pharmacodynamics biomarkers 23

Predictive biomarkers 23

Valid biomarkers 24

Types of biomarkers 24

Genes as biomarkers 24

Proteins as biomarkers 25

Proteomics 25

DNA biomarkers 26

Mitochondrial DNA 26

Mitochondrial mutations 26

RNA biomarkers 26

Transcriptomics 27

MicroRNAs 28

Metabolomics 28

Glycomics 28

Single nucleotide polymorphisms 29

Haplotyping 29

Cell biomarkers of disease 30

Stem cell biomarkers 30

Association of stem cell biomarkers with disease 30

Cancer stem cell biomarkers 30

Endoglin as a functional biomarker of stem cells 31

p75NTR as a biomarker to isolate adipose tissue-derived stem cells 31

Protein expression profile as biomarker of stem cells 31

STEMPRO? EZChek? for analysis of biomarkers of hESCs 32

SSEA-4 as biomarker of MSCs 32

Gaseous mediators as biomarkers of disease 32

Autoantibodies as biomarkers of autoimmune diseases 32

Comparison of various types of biomarkers 33

Biomarkers and systems biology 33

Systems biology approach to biomarker identification 35

Relation of biomarkers to other technologies and healthcare 35

Biomarkers and translational medicine 36

Limitations of use of biomarkers in healthcare 36

2. Technologies for Discovery of Biomarkers 39

Introduction 39

The ideal biomarker 39

Genomic technologies 39

Gene expression 39

Whole genome expression array 40

Gene expression profiling on whole blood samples 41

Profiling gene expression patterns of white blood cells 41

Tissue microarrays for study of biomarkers 41

Epigenomic technologies 42

Discovery of methylation biomarkers 42

Proteomic technologies 43

2D GE 44

Biomarker Amplification Filter 45

CellCarta® proteomics platform 45

Isotope-coded affinity tags 46

Liquid chromatography-MS/MS 46

Lucid Proteomics System 46

Magnetics beads for protein biomarker discovery 47

MASStermind™ 47

Mass spectrometry 47

2D PAGE and mass spectrometry 48

Imaging mass spectrometry 48

MALDI mass spectrometry for biomarker discovery 49

Quantitative tandem MS 50

Single-molecule mass spectrometry using a nanopore 50

Requirements for MS-based proteomic biomarker development 51

Protein tomography 51

Protein biochips/microarrays and biomarkers 51

Antibody-based biomarker discovery 52

Detection of biomarkers using peptide array technology 52

Protein nanobiochip 52

Quantification of protein biomarkers 53

Mass spectrometry for quantification of protein biomarkers 53

Real-time PCR for quantification of protein biomarkers 53

CyTOF for quantification of biomarkers 53

Search for biomarkers in body fluids 54

Challenges and strategies for discovey of protein biomarkers in plasma 54

3-D structure of CD38 as a biomarker 55

BD™ Free Flow Electrophoresis System 55

Isotope tags for relative and absolute quantification 56

Plasma protein microparticles as biomarkers 56

Proteome partitioning 57

Stable isotope tagging methods 57

Technology to measure both the identity and size of the biomarker 58

Biomarkers in the urinary proteome 58

Peptides in body fluids and tissues as biomarkers of disease 58

Analysis of peptides in bodily fluids 59

Serum peptidome patterns 60

SISCAPA method for quantitating proteins and peptides in plasma 60

Comparison of proteomic profiling technologies for discovery of biomarkers 60

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